Looks like a case of cedar-Apple rust. If you're not too attached to the juniper, I'd get rid of it. The infection is systemic, and it will continue to show up. In the spring, it looks like orange slime hanging in the branches. It won't kill junipers quickly, but spreads quickly to apples/malus family.

classic Cedar-Apple rust gall. Brian's comments are spot on. It can not be gotten rid of, and this tree can spread the disease to any member of the apple family you have in your yard or even your neighbor's yard. Burn it or dispose of it miles away from you. (I'm exaggerating, but don't compost this, it can still spread)

Check the crab apples, and apples in you vicinity. it is possible one of them are infected and it spread to your Juniper.